ABSTRACT
RecA is a multifunctional protein that plays a central role in DNA repair in bacteria. The structural Make ATP Work motif (MAW) is proposed to control the ATPase activity of RecA. In the present work, we report the biochemical activity and structural effects of the L53Q mutation at the MAW motif of the RecA protein from H. seropedicae (HsRecA L53Q). In vitro studies showed that HsRecA L53Q can bind ADP, ATP, and ssDNA, as does wild-type RecA. However, the ATPase and DNA-strand exchange activities were completely lost. In vivo studies showed that the expression of HsRecA L53Q in E. coli recA1 does not change its phenotype when cells were challenged with MMS and UV. Molecular dynamics simulations showed the L53Q point mutation did not cause large conformational changes in the HsRecA structure. However, there is a difference on dynamical cross-correlation movements of the residues involved in contacts within the ATP binding site and regions that hold the DNA binding sites. Additionally, a new hydrogen bond, formed between Q53 and T49, was hypothesized to allow an independent motion of the MAW motif from the hydrophobic core, what could explain the observed loss of activity of HsRecA L53Q.
Subject(s)
Adenosine Triphosphate/metabolism , DNA Repair , Herbaspirillum/genetics , Rec A Recombinases/genetics , Adenosine Triphosphatases/metabolism , Amino Acid Motifs , Binding Sites , DNA, Single-Stranded/metabolism , Escherichia coli/metabolism , Escherichia coli/radiation effects , Hydrolysis , Molecular Dynamics Simulation , Point Mutation , Protein Binding , Protein Structure, Tertiary , Rec A Recombinases/chemistry , Rec A Recombinases/metabolism , Ultraviolet RaysABSTRACT
The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament.
Subject(s)
Herbaspirillum/enzymology , Rec A Recombinases/chemistry , Rec A Recombinases/metabolism , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalytic Domain , DNA/genetics , DNA/metabolism , Enzyme Activation , Models, Molecular , Nucleoproteins/chemistry , Nucleoproteins/metabolism , Protein Binding , Protein Conformation , Protein Multimerization , Recombinant Proteins , Static Electricity , Structure-Activity RelationshipABSTRACT
Gamma-ray computed tomography (CT) was employed to study the soil quality of clod samples used to investigate porosity (Ï). Samples with volumes varying from 50 to 100cm(3) were collected from the soil surface. 2D CT images were obtained with millimetric resolution. Porosity distribution analyses were carried out to infer the soil clod structure. Results obtained provided a new insight on the variability of internal clod structure due to the large amount of data analyzed, information that is not provided by traditional methods used in physics applied to soil.
